Tabix files in go.
Bixis a pure go tabix reader. Tabix has a minimum resolution of 16K bases. So, for dense annotations
like ExAC, repeated queries will have to re-parse the same intervals. To mitigate this, Bix caches
all annotations for the blocks from each query and re-uses them for later querires to the same block.
In practice, this results in 10X-100X speedup for any type of data.
tbx, err := bix.New(f)
// Query returns an io.Reader
ph := true // print header ?
rdr, err := tbx.Query(chrom, start, end, ph)
buf := bufio.NewReader(rdr)
for {
line, err := bufr.ReadString('\n')
if err == io.EOF {
break
}
fmt.Println(line)
}
// or
intervals := tbx.Get(chrom, start, end)
where intervals will be either a vcfgo.Variant or an Interval object with a Chrom(), Start(), and End() method.